Modulation of Abeta levels by beta-secretase BACE2

ABSTRACT

The present invention is based on the findings that BACE 2,  a homolog of β-secretase BACE, is able to stimulate processing of APP in a non-amyloidogenic pathway, thereby suppressing the level of Aβ. Accordingly, the present invention provides methods and means for the identification and use of modulators of this unique activity of BACE 2  to suppress Aβ production. The compounds identified using the methods and means provided herein may be used as potential candidates for the treatment of Alzheimer&#39;s disease and other neurological diseases.

[0001] This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application No. 60/215,729 filed Jun. 28, 2000.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention concerns methods and means for the identification and use of modulators of β-amyloid (Aβ) levels obtained by the proteolytic processing of the β-amyloid precursor protein, APP.

[0004] 2. Description of the Related Art

[0005] A number of important neurological diseases, including Alzheimer's disease (AD), cerebral amyloid angiopathy (CAA), and prion-mediated diseases are characterized by the deposition of aggregated proteins, referred to amyloid, in the central nervous system (CNS) (for reviews, see Glenner et al., J. Neurol. Sci. 94:1-28 [1989]; Haan et al., Clin. Neurol. Neurosurg. 92(4):305-310 [1990]). These highly insoluble aggregates are composed of nonbranching, fibrillar proteins with the common characteristic of β-pleated sheet conformation. In the CNS, amyloid can be present in cerebral and meningeal blood vessels (cerebrovascular deposits) and in the brain parenchyma (plaques). Neuropathological studies in human and animal models indicate that cells proximal to amyloid deposits are disturbed in their normal functions (Mandybur, Acta Neuropathol. 78:329-331 [1989]; Kawai et al., Brain Res. 623:142-146 [1993]; Martin et al., Am. J. Pathol. 145:1348-1381 [1994]; Kalaria et al., Neuroreport 6:477-480 [1995]; Masliah et al., J. Neurosci. 16:5795-5811 [1996]; Selkoe, J. Biol. Chem. 271:18295-18298 [1996]; Hardy, Trends Neurosci 20:154-159 [1997]).

[0006] AD and CAA share biochemical and neuropathological markers, but differ somewhat in the extent and location of amyloid deposits as well as in the symptoms exhibited by affected individuals. The neurodegenerative process of AD, the most common neurodegenerative disorder worldwide, is characterized by the progressive and irreversible deafferentation of the limbic system, association neocortex, and basal forebrain accompanied by neuritic plaque and tangle formation (for a review, see Terry et al., “Structural alteration in Alzheimer's disease,” In: Alzheimer's disease, Terry et al. Eds., 1994, pp. 179-196, Raven Press, New York). Dystrophic neurites, as well as reactive astocytes and microglia, are associated with these amyloid-associated neuritic plaques. Although the neuritic population in any given plaque is mixed, the plaques generally are composed of spherical neurites that contain synaptic proteins, APP (type I), and fusiform neurites containing cytoskeletal proteins and paired helical filaments (PHF; type II).

[0007] CAA patients display various vascular syndromes, of which the most documented is cerebral parenchymal hemorrhage. Cerebral parenchymal hemorrhage is the result of extensive amyloid deposition within cerebral vessels (Hardy, Trends Neurosci 20:154-159 [1997]; Haan et al., Clin. Neurol. Neurosurg. 92:305-310 [1990]; Terry et al., [1994] supra; Vinters, Stroke 18:211-224 [1987]; Itoh et al., J. Neurosurgical Sci. 116:135-141 [1993]; Yamada et al., J. Neurol. Neruosurg. Psychiatry 56:543-547 [1993]; Greenberg et al., Neurology 43:2073-2079 [1993]; Levy et al., Science 248:1124-1126 [1990]). In some familial CAA cases, dementia was noted before the onset of hemorrhages, suggesting the possibility that cerebrovascular amyloid deposits may also interfere with cognitive functions.

[0008] Both AD and CAA are characterized by the accumulation of senile plaques in the brains of the affected individuals. The main amyloid components is the amyloid β protein (Aβ), also referred to as amyloid β or β-amyloid peptide, derived from proteolytic processing of the β-amyloid precursor protein, β-APP or simply APP. For review in connection with AD see, Selkoe, D. J. Nature 399: A23-A31 (1999). Aβ is produced by proteolytic cleavage of an integral membrane protein, termed the β-amyloid precursor protein (βAPP).

[0009] The Aβ peptide, which is generated from APP by two putative secretases, is present at low levels in the normal CNS and blood. Two major variants, Aβ₁₋₄₀ and Aβ₁₋₄₂ are produced by alternative carboxy-terminal truncation of APP (Selkoe et al. [1988] Proc. Natl. Acad. Sci. USA 85:7341-7345; Selkoe [1993] Trends Neurosci 16:403-409). Aβ₁₋₄₂ is the more fibrillogenic and more abundant of the two peptides in amyloid deposits of both AD and CAA. In addition to the amyloid deposits in AD cases described above, most AD cases are also associated with amyloid deposition in the vascular walls (Hardy [1997], supra; Haan et al. [1990], supra; Terry et al., [1994] supra; Vinters [1987], supra; Itoh, et al. [1993], supra; Yamada et al. [1993], supra; Greenberg et al. [1993], supra; Levy et al. [1990], supra). These vascular lesions are the hallmark of CAA, which can exist in the absence of AD.

[0010] The precise mechanisms by which neuritic plaques are formed and the relationship of plaque formation to the AD-associated, and CAA-associated neurodegenerative processes are not well defined. However, evidence indicates that dysregulated expression and/or processing of APP gene products or derivatives of these gene products are involved in the pathophysiological process leading to neurodegeneration and plaque formation. For example, missense mutations in APP are tightly linked to autosomal dominant forms of AD (Hardy [1994] Clin. Geriatr. Med. 10:239-247; Mann et al. [1992] Neurodegeneration 1:201-215). The role of APP in neurodegenerative diseases is further implicated by the observation that persons with Down's syndrome who carry an additional copy of the human APP (HAPP) gene on their third chromosome 21 show an overexpression of hAPP (Goodison et al. [1993] J. Neuropathol. Exp. Neurol. 52:192-198; Oyama, et al. [1994] J. Neurochem, 62:1062-1066) as well as a prominent tendency to develop AD-type pathology early in life (Wisniewski et al. [1985] Ann. Neurol. 17:278-282). Mutations in Aβ are linked to CAA associated with hereditary cerebral hemorrhage with amyloidosis (Dutch HCHWA) (Levy, et al. [1990], supra), in which amyloid deposits preferentially occur in the cerebrovascular wall with some occurrence of diffuse plaques (Maat-Schieman et al. [1994] Acta Neuropathol 88:371-8; Wartendorff et al. [1995] J. Neurol. Neurosurg. Psychiatry 58:699-705). A number of HAPP point mutations that are tightly associated with the development of familial AD encode amino acid changes close to either side of the Aβ peptide (for a review, see, e.g., Lannfelt et al. [1994] Biochem. Soc. Trans. 22:176-179; Clark et al. [1993] Arch. Neurol. 50:1164-1172). Finally, in vitro studies indicate that aggregated Aβ can induce neurodegeneration (see, e.g., Pike et al. (1995) J. Neurochem. 64:253-265).

[0011] APP is a glycosylated, single-membrane-spanning protein expressed in a wide variety of cells in many mammalian tissues. Examples of specific isotypes of APP which are currently known to exist in humans are the 695-amino acid polypeptide (APP695) described by Kang et al. (1987) Nature 325:733-736, which is designated as the “normal” APP. A 751-amino acid polypeptide (APP751) has been described by Ponte et al. (1988) Nature 331:525-527 and Tanzi et al. (1988) Nature 331:528-530. A 770-amino acid isotype of APP (APP770) is described in Kitaguchi et al. (1988) Nature 331:530-532. A number of specific variants of APP have also been described having mutations which can differ in both position and phenotype. A general review of such mutations is pivoted in Hardy (1992) Nature Genet. 1:233-235. A mutation of particular interest is designated the “Swedish” mutation where the normal Lys-Met residues at positions 595 and 596 are replaced by Asn-Leu. This mutation is located directly upstream of the normal P-secretase cleavage site of APP, which occurs between residues 596 and 597 of the 695 isotype.

[0012] APP is post-translationally processed by several proteolytic pathways resulting in the secretion of various fragments or intracellular fragmentation and degradation. F. Checler, J. Neurochem. 65:1431-1444 (1995). The combined activity of β-secretase and γ-secretase on APP releases an intact Aβ-amyloid peptide (Aβ), which is a major constituent of amyloid plaques. Initial cleavage of APP by β-secretase generates soluble APPβ and membrane-associated β-CTF that can be further processed by γ-secretase to generate a 40 or a 42 amino acid peptide (Aβ40 or Aβ42). Alternatively, APP processing by α-secretase leads to the formation of soluble APPα and membrane associated α-CTF the latter being a substrate for γ-secretase to generate the non-amyloidogenic p3. Aβ is an approximately 43 amino acid peptide, which comprises residues 597-640 of the 695 amino acid isotype of APP. Internal cleavage of Aβ by a α-secretase inhibits the release of the full-length Aβ peptide. Although the extent of pathogenic involvement of the secretases in AD progression is not fully elucidated, these proteolytic events are known to either promote or inhibit Aβ formation, and thus are thought to be good therapeutic candidates for AD.

[0013] The polytopic transmembrane protein presenilin has been strongly implicated in γ-secretase activity (for review see Haass and De Strooper, Science 286: 916-919 [1999]). Mutagenesis of two transmembrane aspartates of presenilin led to the inactivation of γ-secretase activity in cellular assays (Wolfe et al., Nature 398: 513-517 [1999]). As a result, both α- and β-CTFs accumulated and Aβ formation was significantly decreased. Similar effects were seen upon inhibition of γ-secretase using substrate analogs (Wolfe et al., J. Med. Chem. 41: 6-9 [1998]). While it remains to be determined whether presenilin is sufficient as γ-secretase or whether it requires another unique co-factor of so far unknown nature to exert its function Presenilin 1 and γ-secretase activity have recently been shown to co-precipitate from membrane extracts (Li et al. Proc. Natl. Acad Sci. USA 97(11):6138-43 [2000]).

[0014] As discussed above, there are at least two proteases involved in the generation of Aβ, referred to as β- and γ-secretases (Citron et al., Neuron 17:171-179 [1996]; Seubert et al., Nature 361:260-263 [1993]; Cai et al., Science 259:514-516 [1993]; and Citron et al., Neuron 14:661-670 [1995]). There have been intense efforts in recent years to identify and characterize these enzymes. Recently five independent groups have reported cloning and characterization of genes corresponding to a β-secretase (Vassar et al., Science 286: 735-741 [1999]; Yan et al., Nature 402: 533-537 [1999]; Sinha et al., Nature 402: 537-540 [1999]; Hussain et al., Mol. Cell. Neurosci. 14: 419-427 [1999]; Lin et al. Proc. Natl. Acad. Sci. USA 97: 1456-1460 [2000]). The membrane-bound aspartyl protease has been variously referred to as β-site APP-cleaving enzyme (BACE), Aspartyl protease-2 (Asp2), memapsin 2 or simply as β-secretase . However, the deduced amino acid sequence of the polypeptide chain reported by all five groups is identical. The cloned enzyme possesses many of the characteristics expected of an authentic β-secretase. In particular, BACE overexpression resulted in an increase in both β-NTF and Aβ levels while suppression of BACE with antisense oligonucleotides led to a significant reduction of these cleavage products. As predicted for the genuine β-secretase, the Swedish double mutant of APP (APPsw, Mullan et al., Nature Genetics 1: 345-347 [1992]; Citron et al, Nature 360: 672-674 [1992]; Cai et al., Science 259: 514-516 [1993]) was cleaved more efficiently by BACE. Taken together, these results have led to the notion that BACE is the main β-secretase activity.

[0015] A close homolog of BACE, designated DRAP or BACE2, has been described recently (Acquati et al., FEBS Lett. 468: 59-64 [2000], GenBank accession numbers for the human and mouse cDNA sequences: AF050171 and AF051150, respectively; Bennett et al., J. Biol. Chem. 275:37712-7 [2000]). BACE and BACE2 share 64% amino acid similarity but the role of BACE2 in APP processing has not yet been elucidated. Strikingly, BACE2 expression in brain appears to be very low and this observation has contributed to the assumption that BACE2's role in β-secretase cleavage might only be minor (Bennett et al., ibid).

SUMMARY OF THE INVENTION

[0016] Experimental data disclosed herein confirm that BACE2 indeed possesses β-secretase activity when reconstituting β-secretase cleavage in a cell-free assay using wild-type (wt) or Swedish mutant forms of APP751 as a substrate. However, this activity is weaker than the β-secretase activity of BACE. The invention is further based on the unexpected finding that while BACE2 overexpression in HEK293 cells had a moderate effect on β-NTF formation, it strikingly suppressed Aβ production in either the presence or absence of additional exogenous copies of BACE. BACE2 also modulated Aβ levels in neuronal SKN cells and thus its effect was not restricted to non-neuronal HEK293 cells. The suppression of Aβ production by BACE2 did not appear to require its ability to cleave at the β-secretase site. Aβ levels were similarly suppressed in cells carrying a C-terminal 100 amino acids fragment of amyloid precursor protein (APP) truncated to mimic β-secretase cleavage. It is suggested that BACE2 functions as a modulator of Aβ production by promoting the alternative non-amyloidogenic APP processing pathway such as that mediated by α-secretase activity.

[0017] In one aspect, the invention concerns a method of modulating the enzymatic production of Aβ-amyloid peptide (Aβ) from β-amyloid precursor protein (APP) or a fragment thereof by contacting said APP or APP fragment with a BACE2 polypeptide or an agonist or antagonist thereof. In a specific embodiment, the method concerns the inhibition of Aβ production from APP or an APP fragment by using BACE2 or an agonist of BACE2.

[0018] In another aspect, the invention concerns a method of inhibiting the formation of an Aβ-amyloid peptide (Aβ) from Aβ-amyloid precursor protein (APP) or a fragment thereof by contacting APP of an APP fragment with a BACE2 polypeptide or an agonist thereof.

[0019] In yet another aspect, the invention concerns a method of inhibiting the release of a full-length β-amyloid (Aβ) polypeptide from β-amyloid precursor protein (APP) or a fragment thereof, comprising cleaving said APP or APP fragment by a BACE2 polypeptide or an agonist thereof at a site interfering with '-secretase processing of the APP or APP fragment.

[0020] In all aspects, APP may, for example, be a native sequence human APP including the 695-amino acid isotype and the isotype containing the so called Swedish mutation. The APP fragment specifically includes, without limitation, β-CTF. The methods may be performed in the presence of an α-secretase activity and/or a γ-secretase activity and/or a β-secretase activity other than BACE2. The additional β-secretase activity may, for example, be due to the presence of an enzyme having a pH optimum at about pH 6.5-7.0, and an estimated molecular weight of about 32-39 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts, or about 20-26 kDa as calculated from radiation inactivation analysis of human brain samples, with a candidate compound. Alternatively or in addition, the additional β-secretase activity may be due to the presence of a β-secretase enzyme having a pH optimum at about pH 4.5-5.0 and an estimated molecular weight of about 50-60 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts or human brain samples (BACE1). These β-secretase activities are further disclosed and characterized in co-pending application Ser. No. 09/566,746 filed on May 9, 2000 for Novel β-Secretase and Modulation of β-Secretase Activity (attorney docket no: SCIOS.020A) the entire disclosure of which is hereby expressly incorporated by reference.

[0021] In a further aspect, the invention concerns a method for identifying a modulator of the enzymatic production of β-amyloid peptide (Aβ) from β-amyloid precursor protein (APP) or a fragment thereof, comprising contacting APP or an APP fragment and BACE2 with a candidate compound and monitoring the effect of the candidate compound on the production of Aβ. In a preferred embodiment, the method is used to identify inhibitors of the enzymatic production of Aβ from APP or a fragment thereof. The effect of the candidate compound on the production of Aβ may, for example, be monitored by measuring the amount of Aβ formed but other method of monitoring are also within the scope of the invention. In a preferred embodiment, the method is used to identify inhibitors that reduce the amount of Aβ formed by at least about 50%, preferably by at least about 75%, more preferably by at least about 85%, most preferably by at least about 90%.

[0022] Just as in the previous aspects, APP may, for example, be a native sequence human APP including the 695-amino acid isotype and the isotype containing the so called Swedish mutation. The APP fragment specifically includes, without limitation, β-CTF . The method may be performed in the presence of an α-secretase activity and/or a γ-secretase activity and/or a β-secretase activity other than BACE2. The additional β-secretase activity may, for example, be due to the presence of an enzyme having a pH optimum at about pH 6.5-7.0, and an estimated molecular weight of about 32-39 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts, or about 20-26 kDa as calculated from radiation inactivation analysis of human brain samples, with a candidate compound. Alternatively or in addition, the additional β-secretase activity may be due to the presence of a β-secretase enzyme having a pH optimum at about pH 4.5-5.0 and an estimated molecular weight of about 50-60 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts or human brain samples (BACE1).

[0023] In a still further aspect, the invention concerns a modulator of the enzymatic production of Aβ-amyloid peptide (Aβ) from Aβ-amyloid precursor protein (APP) or a fragment thereof, identified by the foregoing method. The modulator preferably is an inhibitor, and may, for example, be a polypeptide, peptide, or small molecule.

[0024] In an additional aspect, the invention concerns a method for reducing the amount of Aβ-amyloid deposits in the central nervous system (CNS) of a mammal comprising administering to the mammal an effective amount of BACE2 or an agonist thereof.

[0025] In another aspect, the invention concerns a method for the treatment of Alzheimer's disease (AD), an AD-type pathology or cerebral amyloid angiopathy in a mammalian patient, comprising administering to the patient an effective amount of BACE2 or an agonist thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

[0026]FIG. 1. BACE2 possesses β-secretase activity in vitro. β-secretase cleavage was reconstituted at pH 4.5 using extracts derived from BACE and BACE2 as well as mock-transfected HEK293T cells. The kinetics of β-NTF formation using partially purified native APP751sw (a) and APP751 (b) as a substrate are shown.

[0027]FIG. 2. BACE2 leads to alternative processing of APP and suppresses Aβ formation in HEK293T cells. Different amounts of BACE and BACE2 cDNA were co-transfected with constant levels of APP751sw plasmid and conditioned medium was analyzed for β-NTF (a), α-NTF (b), total Aβ (c) and Aβ42 (d) 72 hours post-transfection. BACE2 shows some β-secretase activity in vivo while dramatically suppressing the production of Aβ40 and Aβ42. The metabolism of APP CTFs was analyzed in a parallel pulse-chase experiment (e). Transfected cells were labelled for 15 minutes with 200 μCi Promix L [³⁵S] (Amersham) and chased for up to 90 minutes. APP and CTFs were immunoprecipitated as described. Full length mature and immature APP (APP) as well as bands corresponding to β-CTF , alternatively cleaved β′-CTF and α-CTF are shown. The formation of Aβ and p3 was analyzed in a pulse-labeling experiment (f). Transfected cells were labeled for 5 hours with 300 μCi Promix L [³⁵S] (Amersham) and conditioned medium was precipitated with antibodies directed against the C-terminal residues of Aβ40 and Aβ42, respectively, that also recognize the corresponding p3 forms. The arrow indicates an additional Aβ species derived from cleavage of the β′-CTF in BACE transfected cells.

[0028]FIG. 3. Increasing doses of BACE2 differentially affect cleavage at the β-secretase site and Aβ formation. Constant amounts of BACE and increasing amounts of BACE2 were co-transfected with APP751sw into HEK293T cells. Conditioned medium was analyzed for β-NTF (a) and Aβ (b) formation as described.

[0029]FIG. 4. BACE2 shows β-secretase activity and suppresses Aβ formation in SK-N-MC cells. Different amounts of BACE and BACE2 cDNA were co-transfected with constant levels of APP751sw plasmid and conditioned medium was analyzed for—NTF (a), total A (b) and Aβ42 (c) 72 hours post-transfection.

[0030]FIG. 5. Prior β-secretase cleavage is not required for Aβ suppression by BACE2. BACE and BACE2 were co-transfected with CT100, an APP construct that mimics prior β-secretase cleavage and total Aβ (a) and Aβ42 (b) were measured in conditioned medium by ELISA. The conditioned medium was further subjected to Western blotting for the detection of Aβ and CTFs (c) as described. The metabolism of CT100 was analyzed in a parallel pulse-chase experiment (d). Cells were labeled for 15 minutes with 200 μCi Promix L [35S] (Amersham) and chased for up to 90 minutes. CTFs were immunoprecipitated as described. CT1O0 as well as the α-CTF-like band are shown.

[0031]FIG. 6. Mutation of the conserved aspartate residue in BACE2 abolishes β-secretase activity in vitro and reverses the effect on Aβ formation in vivo. Membrane extracts from BACE2, BACE2 D110A, or mock-transfected HEK293T cells were separated on Q-HP-Sepharose and fractions were reconstituted with APP751sw substrate for 2 hours at 37° C. β-NTF formation was monitored as described (a). BACE2 D110A and wildtype BACE2 were co-transfected with APP751sw or CT100 in HEK293T cells. Total Aβ (b), Aβ42 (c), and β-NTF (d) were determined in conditioned medium as described.

[0032]FIG. 7 shows the nucleotide sequence of human BACE2 (SEQ ID NO: 1).

[0033]FIG. 8 shows the deduced amino acid sequence of human BACE2 (SEQ ID NO: 2).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

[0034] A wide variety of proteins may be involved in the processing or regulation of processing of βAPP in order to generate β-Amyloid (Aβ) peptide, the aggregation and extracellular deposition of which in the brain is a hallmark of Alzheimer's disease pathology. Therefore, any therapeutic strategy evolved to prevent, delay, slow down or halt the deposition of these plaques in Alzheimer's patients should take into account not only the activities of various secretases, but also various proteins involved the regulation or modulation of such enzymes. A novel activity of BACE2 as disclosed herein provides yet another target for screening of compounds to identify potential drug candidates for the treatment (including prevention) of Alzheimer's disease and other neurodegenerative disorders. The present invention provides a way for screening of agonists or activators of BACE2-mediated suppression of Aβ peptide, and for the identification of potential drugs for Alzheimer's disease.

I. DEFINITIONS

[0035] Before the present invention is described, it is to be understood that this invention is not limited to particular methodology described. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

[0036] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.

[0037] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.

[0038] As used herein, “β-amyloid precursor protein” (APP or βAPP) refers to a polypeptide that is encoded by a gene of the same name localized in humans on the long arm of chromosome 21 and that includes a β-amyloid protein region within its carboxy terminal region.

[0039] The term “BACE2” is used herein to refer to native sequence BACE2 from any animal, e.g. mammalian, species, including humans, and BACE2 variants (which are further defined below). The BACE2 polypeptides may be isolated from a variety of sources, including human tissue types or prepared by recombinant and/or synthetic methods.

[0040] “Native sequence BACE2” refers to a polypeptide having the same amino acid sequence as a BACE2 polypeptide occurring in nature regardless of its mode of preparation. A native sequence BACE2 may be isolated from nature, or prepared by recombinant and/or synthetic methods. The term “native sequence BACE2” specifically encompasses naturally occurring truncated or secreted forms, naturally occurring variant forms (e.g. alternatively spliced forms), and naturally occurring allelic variants of BACE2, whether known or to be discovered in the future.

[0041] The term “BACE2 variant” refers to amino acid sequence variants of a native sequence BACE2, containing one or more amino acid substitution and/or deletion and/or insertion in the native sequence. The amino acid sequence variants generally have at least about 75%, preferably at least about 80%, more preferably at least about 85%, even more preferably at least about 90%, most preferably at least about 95% sequence identity with the amino acid sequence of a native sequence BACE2.

[0042] “Sequence identity” is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a native sequence polypeptide after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of sequence identity. The % sequence identity values are generated by NCBI BLAST2.0 software as defined by Altschul et al. (1997), Nucleic Acids Res. 25:3389-3402. In a preferred embodiment, an amino acid sequence variant of a native sequence BACE2 is encoded by nucleic acid hybridizing under stringent conditions to the complement of the nucleic acid shown in FIG. 7 (SEQ ID NO: 1), and retains a biological activity of a native sequence BACE2.

[0043] “Stringent” hybridization conditions are sequence dependent and will be different with different environmental parameters (e.g., salt concentrations, and presence of organics). Generally, stringent conditions are selected to be about 5° C. to 20° C. lower than the thermal melting point (T_(m)) for the specific nucleic acid sequence at a defined ionic strength and pH. Preferably, stringent conditions are about 5° C. to 10° C. lower than the thermal melting point for a specific nucleic acid bound to a complementary nucleic acid. The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of a nucleic acid (e.g., tag nucleic acid) hybridizes to a perfectly matched probe

[0044] “Stringent” wash conditions are ordinarily determined empirically for hybridization of each set of tags to a corresponding probe array. The arrays are first hybridized (typically under stringent hybridization conditions) and then washed with buffers containing successively lower concentrations of salts, or higher concentrations of detergents, or at increasing temperatures until the signal to noise ratio for specific to non-specific hybridization is high enough to facilitate detection of specific hybridization. Stringent temperature conditions will usually include temperatures in excess of about 30° C., more usually in excess of about 37° C., and occasionally in excess of about 45° C. Stringent salt conditions will ordinarily be less than about 1000 mM, usually less than about 500 mM, more usually less than about 400 mM, typically less than about 300 mM, preferably less than about 200 mM, and more preferably less than about 150 mM. However, the combination of parameters is more important than the measure of any single parameter. See, e.g., Wetmur et al., J. Mol. Biol. 31:349-70 (1966), and Wetmur, Critical Reviews in Biochemistry and Molecular Biology ,26(34):227-59 (1991). In a preferred embodiment, “stringent conditions” or “high stringency conditions,” as defined herein, may be hybridization in 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

[0045] The term “recombinant” when used with reference to a cell, animal, or virus indicates that the cell, animal, or virus encodes a foreign DNA or RNA. For example, recombinant cells optionally express nucleic acids (e.g., RNA) not found within the native (non-recombinant) form of the cell.

[0046] “Mammal” for purposes of the present inventin refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. Preferably, the mammal herein is human.

[0047] The term “biological activity” in connection with BACE2 is used to refer to the ability of a BACE2 molecule (including variants of native sequence BACE2) to modulate, preferably suppress the enzymatic production of β-amyloid peptide (Aβ) from the β-amyloid precursor protein (APP) or a fragment thereof, irrespective of the mechanism by which the modulation (suppression) occurs. In a preferred embodiment, the BACE2 “biological activity” is the ability to inhibit β-amyloid formation from native sequence APP or a fragment thereof, including fragment(s) obtained by β-secretase processing, e.g. β-CTF (CT100). In another preferred embodiment, BACE 2 “biological activity” is the ability to cleave APP or a fragment thereof (including, but not limited to β-CTF) such that the release of a full-length Aβ peptide by further enzymatic processing is inhibited.

[0048] The term “BACE2 agonist” or “agonist of BACE2 (biological) activity” is used in the broadest sense and refers to a molecule that stimulates the production of a native sequence BACE2, enhances a biological activity of a native sequence BACE2 and/or mimics a biological activity of a native sequence BACE2. Thus, a BACE2 agonist may specifically change the function and/or expression of a native sequence BACE2 polypeptide, or the efficiency of signaling through a pathway involving a native sequence BACE2 polypeptide.

[0049] Similarly, the term “BACE2 antagonist” or “antagonist of BACE2 activity” is used in the broadest sense and includes any molecule that partially or fully blocks, inhibits or neutralizes a biological activity of a native sequence BACE2 polypeptide.

[0050] The terms “Aβ-amyloid protein”, “amyloid β protein”, “β-amyloid peptide”, “amyloid β peptide” and “Aβ”, which are used interchangeably, refer to all β-amyloid peptides or polypeptides generated by N-terminal proteolysis of APP followed by carboxy-terminal truncation, including any peptide or polypeptide containing from about 38 to about 44 amino acids, inclusive, and preferably comprising residues 597-640 of the 695 amino acid isotype human APP, including, without limitation, the two major variants, Aβ₁₋₄₀ and Aβ₁₋₄₂, as well as corresponding regions of other isotypes of human APP and non-human mammalian homologues of APP. After this disclosure others will, perhaps, discover other Aβ-amyloid proteins, all of which are all intended to come within the scope of the present invention.

[0051] The term p3 peptide refers to the approximately 26 amino acid segment resulting from α-secretase activity, generally occurring between residues 612 and 613 of the 695 APP isoform and the heterogeneous γ-secretase cleavge of APP in the region of residue 638 to 640 of the 695 amino acid isotype human APP.

[0052] The terms “APP secretase,” “secretase” and “secretase activity” as used interchangeably herein refer to any proteolytic enzyme and/or activity which results in the secretion of various fragments or intracellular fragmentation and degradation of APP. This includes α-secretase, β-secretase, γ-secretase, and any similar but as of yet unidentified enzymes, which cause the proteolysis of either APP or Aβ.

[0053] The terms “β-secretase ” and “β-secretase activity” as used interchangeably herein refer to the enzyme or enzymes responsible for proteolysis of APP at the N-terminal cleavage site of APP, which occurs between residues 596 and 597 of the 695 isotype of APP (Kang et al. (1987) Nature 325:733-736) and between residues 652 and 653 of the 751 isotype of APP (Ponte et al. (1988) Nature 331:525-527). A secondary cleavage by β-secretase occurs between residues 605 and 606 of the 695 APP isoform and between residues 661 and 662 of the 751 APP isoform (Higaki et al. (1996) Neuron 14:651-659). The terms are used in the broadest sense and include isolated, partially or fully purified, recombinantly produced enzymes, cells or cell preparations (including membrane preparations) comprising a β-secretase enzyme, and any solution or mixture comprising a β-secretase enzyme.

[0054] The term “APP/β-secretase mixture” as used herein refers to the isolated APP and β-secretase as a complex and/or as a mixture of the two substances.

[0055] The term “α-secretase” and “α-secretase activity” are used interchangeably, and refer to the enzyme or enzymes capable of producing a cleavage within the β-amyloid domain of APP or the C-terminal fragment of APP resulting from β-secretase processing. The processing by α-secretase activity, generally occurs between residues 612 and 613 of the 695 APP isoform or between residues 16 and 17 of the C-terminal fragment of APP resulting from β-secretase processing. The terms are used in the broadest sense and include isolated, partially or fully purified, recombinantly produced enzymes, cells or cell preparations (including membrane preparations) comprising an α-secretase enzyme, and any solution or mixture comprising a α-secretase enzyme.

[0056] The terms “γ-secretase ” and “γ-secretase activity” are used interchangeably, and refer to the enzyme or enzymes responsible for generating the C-termini of the β-amyloid peptides and p3 peptide by cleaving within the transmembrane region of APP. The terms are used in the broadest sense and include isolated, partially or fully purified, recombinantly produced enzymes, cells or cell preparations (including membrane preparations) comprising an γ-secretase enzyme, and any solution or mixture comprising a γ-secretase enzyme.

[0057] The term “Alzheimer's disease” (abbreviated herein as “AD”) as used herein refers to a condition associated with formation of neuritic plaques comprising β-amyloid protein primarily in the hippocampus and cerebral cortex, as well as impairment in both learning and memory. “AD” as used herein is meant to encompass both AD as well as AD-type pathologies.

[0058] The term “AD-type pathology” as used herein refers to a combination of CNS alterations including, but not limited to, formation of neuritic plaques containing β-amyloid protein in the hippocampus and cerebral cortex. Such AD-type pathologies can include, but are not necessarily limited to, disorders associated with aberrant expression and/or deposition of APP, overexpression of APP, expression of aberrant APP gene products, and other phenomena associated with AD. Exemplary AD-type pathologies include, but are not necessarily limited to, AD-type pathologies associated with Down's syndrome that is associated with overexpression of APP.

[0059] The term “phenomenon associated with Alzheimer's disease” as used herein refers to a structural, molecular, or functional event associated with AD, particularly such an event that is readily assessable in an animal model. Such events include, but are not limited to, amyloid deposition, neuropathological developments, learning and memory deficits, and other AD-associated characteristics.

[0060] The term “cerebral amyloid angiopathy” (abbreviated herein as CAA) as used herein refers to a condition associated with formation of amyloid deposition within cerebral vessels which can be complicated by cerebral parenchymal hemorrhage. CAA is also associated with increased risk of stroke as well as development of cerebellar and subarachnoid hemorrhages (Vinters (1987) Stroke 18:311-324; Haan et al. (1994) Dementia 5:210-213; Itoh, et al. (1993) J. Neurol. Sci. 116:135-414). CAA can also be associated with dementia prior to onset of hemorrhages. The vascular amyloid deposits associated with CAA can exist in the absence of AD, but are more frequently associated with AD.

[0061] The term “phenomenon associated with cerebral amyloid angiopathy” as used herein refers to a molecular, structural, or functional event associated with CAA, particularly such an event that is readily assessable in an animal model. Such events include, but are not limited to, amyloid deposition, cerebral parenchymal hemorrhage, and other CAA-associated characteristics.

[0062] The term “Aβ-amyloid deposit” as used herein refers to a deposit in the brain composed of Aβ as well as other substances.

[0063] The term “non-amyloidogenic” refers to a process which reduces or eliminates the production of Aβ-amyloid.

[0064] By “antibody” is meant an immunoglobulin protein which is capable of binding an antigen. Antibody as used herein is meant to include the entire antibody as well as any antibody fragments (e.g., F(Ab′)₂, Fab′, Fab, Fv) capable of binding the epitope, antigen or antigenic fragment of interest.

[0065] Antibodies of the invention are immunoreactive or immunospecific for and therefore specifically and selectively bind specific proteolytic products of the APP protein. Antibodies for each proteolytic product are preferably immunospecific - i.e., not substantially cross-reactive with other proteolytic products of APP. The term “antibody” encompasses all types of antibodies both polyclonal and monoclonal antibodies, and produced using a suitable, e.g. peptide antigen.

[0066] By “purified antibody” is meant one which is sufficiently free of other proteins, carbohydrates, and lipids with which it is naturally associated. Such an antibody “preferentially binds” to a proteolytic APP protein product (or an antigenic fragment thereof), i.e., does not substantially recognize and bind to other antigenically-unrelated molecules. A purified antibody of the invention is preferably immunoreactive with and immunospecific for a particular APP protein product (e.g., βNTF) and more preferably will not react with other APP protein products.

[0067] By “antigenic fragment” of an APP proteolytic product is meant a portion of such a protein which is capable of binding an antibody used in the assay of the invention.

[0068] By “binds specifically” is meant high avidity and/or high affinity binding of an antibody to a specific polypeptide, i.e., epitope of a APP protein product. Antibody binding to its epitope on this specific polypeptide is preferably stronger than binding of the same antibody to any other epitope, particularly those which may be present in molecules in association with, or in the same sample, as the specific polypeptide of interest, e.g., binds more strongly to APP protein product than other epitopes so that by adjusting binding conditions the antibody binds almost exclusively to the APP protein product. Antibodies which bind specifically to a polypeptide of interest may be capable of binding other polypeptides at a weak, yet detectable, level (e.g., 10% or less of the binding shown to the polypeptide of interest). Such weak binding, or background binding, is readily discernible from the specific antibody binding to the compound on polypeptide of interest, e.g., by use of appropriate controls. In general, antibodies of the invention bind to a particular APP protein product with a binding affinity of 10⁷ moles/liter or more, preferably 10⁸ mole/liters or more. In general, an antibody with a binding affinity of 10⁶ moles/liter or less is not useful in that it will not bind antigen at a detectable level using conventional methodology currently used.

[0069] By “detectably labeled antibody” or “detectably labeled anti-βNTF” is meant an antibody (or antibody fragment which retains binding specificity), having an attached detectable label. The detectable label is normally attached by chemical conjugation, but where the label is a polypeptide, it could alternatively be attached by genetic engineering techniques. Methods for production of detectably labeled proteins are well known in the art. Detectable labels may be selected from a variety of such labels known in the art, but normally are radioisotopes, fluorophores, paramagnetic labels, enzymes (e.g., horseradish peroxidase), or other moieties or compounds which either emit a detectable signal (e.g., radioactivity, fluorescence, color) or emit a detectable signal after exposure of the label to its substrate. Various detectable label/substrate pairs (e.g., horseradish peroxidase/diaminobenzidine, avidin/streptavidin, luciferase/luciferin), methods for labeling antibodies, and methods for using labeled antibodies are well known in the art (see, for example, Harlow and Lane, eds. (Antibodies: A Laboratory Manual (1988) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

[0070] The term “compound” as used herein describes any molecule, e.g., protein, naturally occurring substances, synthesized protein or small molecule pharmaceutical, with the capability of affecting secretase activity. Such compounds may be used to treat the molecular and clinical phenomena associated with amyloid-associated disorders, and specifically AD, CAA and prion-medicated disorder.

[0071] The terms “effective dose”, “effective amount” and “amount effective” are used interchangeably, and refer to an administration of a compound sufficient to provide the desired physiological and/or psychological change. This will vary depending on the patient, the disease and the treatment. The dose may either be a therapeutic dose, in which case it should sufficiently alter levels of amyloid plaques in the subject to alleviate or ameliorate the symptoms of the disorder or condition, or a prophylactic dose, which should be sufficient to prevent accumulation of amyloid plaques to an undesirable level. The terms “treatment,” “treating” and the like are used herein to generally mean obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. “Treatment” as used herein covers any treatment of a disease in a mammal, particularly a human, and includes:

[0072] (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it;

[0073] (b) inhibiting the disease, i.e., arresting its development; or

[0074] (c) relieving the disease, i.e., causing regression of the disease. The therapeutic agents that can be identified using the assay of the invention are particularly useful in the treatment of any disease associated with the deposition of β-amyloid, including AD, hereditary cerebral hemorrhage with amyloidosis, and prion-mediated disorders, and the like.

[0075] The terms “modulate”, “alter” and grammatical variants thereof, when used in connection with the methods of the present invention, include any and all modifications, such as inhibition or enhancement of β-secretase activity.

II. DESCRIPTION OF PREFERRED EMBODIMENTS

[0076] 1. Inhibition of β-amyloid production by BACE2 or stimulators of BACE2 activity.

[0077] In one aspect, the invention concerns a method for inhibiting Aβ-amyloid formation from APP or the β-secretase product or products of APP by treating APP with an effective amount of BACE2 or a stimulator of BACE2 activity. In this method BACE2 can be any native BACE2 polypeptide, including all isoforms and allelic variants of native human and non-human mammalian BACE2 polypeptides, known or hereinafter identified, as well as any biologically active variant thereof as hereinabove defined. The treatment may be performed in vitro or in vivo. Stimulators of BACE2 activity may be identified as described hereinbelow.

[0078] When the treatment is performed in vivo, its objective is the treatment (including prevention) of a neurological disease characterized by the deposition of β-amyloid in the central nervous system. Such diseases include, without limitation, Alzheimer's disease (AD) and AD-type pathologies, including, but not limited to, pathologies associates with Down's syndome, as well as cerebral amyloid angiopathy, whether associated with or existing in the absence of Alzheimer's disease.

[0079] In general, BACE2 or a compound identified in an assay described hereinbelow, will reduce the level of β-amyloid plaque in the brain tissue of a mammalian host, including humans. In general, the compounds enhancing the ability of BACE2 to promote non-amyloidogenic cleavage of APP will reduce the level of Aβ-amyloid plaque in brain tissue by enhancing in vivo levels of BACE2-mediated suppression of Aβ production. Therapeutic effects may be seen, for example, by compounds that increase the expression level of BACE2 protein or enhance or activate BACE2-mediated non-amyloidogenic α-secretase-like processing of APP or fragments of APP, resulting in reduced Aβ production. Prophylactic use is also contemplated for individuals at risk of developing Alzheimer's disease (AD), AD-type pathologies and/or cerebral amyloid angiopathy, such as the elderly and/or individuals carrying known mutations linked to AD.

[0080] In the in vivo treatment methods, BACE2 or other compounds of the present invention may be administered to the host using any convenient means capable of resulting in the desired target protein activity modulation. Thus, the compound can be incorporated into a variety of formulations for therapeutic administration. More particularly, the compounds of the present invention can be formulated into pharmaceutical compositions by combination with appropriate, pharmaceutically acceptable carriers or diluents, and may be formulated into preparations in solid, semi-solid, liquid or gaseous forms, such as tablets, capsules, powders, granules, ointments, solutions, transdermal patches, suppositories, injections, inhalants and aerosols.

[0081] As such, administration of the compounds can be achieved in various ways, including oral, buccal, rectal, parenteral, intraperitoneal, intravaginal, intradermal, transdermal, intratracheal, etc., administration.

[0082] In pharmaceutical dosage forms, the compounds may be administered in the form of their pharmaceutically acceptable salts, or they may also be used alone or in appropriate association, as well as in combination, with other pharmaceutically active compounds. The following methods and excipients are merely exemplary and are in no way limiting.

[0083] For oral preparations, the compounds can be used alone or in combination with appropriate additives to make tablets, powders, granules or capsules. Examples of additives are conventional additives, such as lactose, mannitol, corn starch or potato starch; binders, such as crystalline cellulose, cellulose derivatives, acacia, corn starch or gelatins; disintegrators, such as corn starch, potato starch or sodium carboxymethylcellulose; lubricants, such as talc or magnesium stearate; and if desired, diluents, buffering agents, moistening agents, preservatives and flavoring agents.

[0084] The compounds of the invention can be formulated into preparations for injection by dissolving, suspending or emulsifying them in an aqueous or nonaqueous solvent, such as vegetable or other similar oils, synthetic aliphatic acid glycerides, esters of higher aliphatic acids or propylene glycol. If desired, conventional additives such as solubilizers, isotonic agents, suspending agents, emulsifying agents, stabilizers and preservatives may also be added. The concentration of therapeutically active compound in the formulation may vary from about 0.5-100 wt. %.

[0085] The compounds can be utilized in aerosol formulation to be administered via inhalation. The compounds of the present invention can be formulated into pressurized acceptable propellants such as dichlorodifluoromethane, propane, nitrogen and the like.

[0086] Furthermore, the compounds can be made into suppositories by mixing with a variety of bases such as emulsifying bases or water-soluble bases. The compounds of the present invention can be administered rectally via a suppository. The suppository can include vehicles such as cocoa butter, carbowaxes and polyethylene glycols, which melt at body temperature, yet are solidified at room temperature.

[0087] Unit dosage forms for oral or rectal administration such as syrups, elixirs, and suspensions may be provided wherein each dosage unit (e.g., a teaspoonful, tablespoonful, tablet or suppository) contains a predetermined amount of the composition containing one or more inhibitors. Similarly, unit dosage forms for injection or intravenous administration may comprise the inhibitor(s) in a composition as a solution in sterile water, normal saline or another pharmaceutically acceptable carrier.

[0088] The pharmaceutically acceptable excipients, such as vehicles, adjuvants, carriers or diluents, are readily available to the public. Moreover, pharmaceutically acceptable auxiliary substances, such as pH adjusting and buffering agents, tonicity adjusting agents, stabilizers, wetting agents and the like, are readily available to the public.

[0089] The compounds are administered to a host in a physiologically acceptable carrier, at a dosage from 5 mg to 1400 mg, more usually from 100 mg to 1000 mg, preferably 500 mg to 700 mg for a dose of 0.5 to 20 mg/kg weight. The dosage for compounds altering (modulating, e.g. enhancing or inhibiting) BACE2 activity is elected so that the BACE2 activity is altered by 10 to 80%, more preferably 20 to 70% and even more preferably 25-50%.

[0090] 2. Screening assays

[0091] In another aspect, the present invention provides screening assays for identifying modulators (including stimulators and inhibitors) of the ability of BACE2 to interfere with APP amyloidogenic processing resulting in the modulation (e.g. suppression) of Aβ production. BACE2, APP and processing secretases, any or all of which may be present in isolated, immobilized or cell bound form or in the form of membrane-enzyme mixture, are contacted with a candidate compound, or a plurality of candidate compounds, and those candidates are selected that alter, preferably enhance, BACE2-mediated reduction of Aβ production. While the effect of a candidate compound on BACE2 activity is preferably detected by monitoring its ability to alter (e.g. reduce) the amount of Aβ produced, other read-outs of APP or APP fragments cleavage at the α, β or γ-secretase cleavage sites are equally suitable. Both cell-free and cell based assays, including assays performed with cell membrane-enzyme preparations are specifically within the scope of the invention.

[0092] Candidate compounds which significantly enhance the expression or the ability of BACE2 to promote APP cleavage at or around the α-secretase cleavage site are preferred. Such compounds preferably enhance the expression or the ability of BACE2 to reduce the amount of Aβ produced, or any other read-out indicative of α-secretase mediated cleavage of APP, by at least about 25%, preferably at least about 50%, more preferably at least about 75%, most preferably at least about 90%, and often at least about 95%. The compounds identified can be used in the treatment of patients, particularly humans, at risk of developing or diagnosed with AD, AD-type pathologies, cerebral amyloid angiopathy or any other pathology associated with the formation of β-amyloid deposits (e.g. plaques) in the CNS, such as brain.

[0093] In one particular embodiment, the assay involves contacting APP or APP fragments of β-secretase processing or the C-terminal 100 residues of APP/BACE2 as individual components or as a mixture or complex with a test compound, and thereafter determining the level of soluble product of APP proteolysis, particularly Aβ and/or β-NTF and/or p3 and/or α-CTF. In cell-based assays, including assays using membrane preparations, cell membranes (obtained by cell lysis) may be additionally assayed for cell-associated products of APP proteolysis, i.e. CTFs (α-CTF and/or β-CTF ). The APP and BACE2 which are contacted with the compound can be both isolated from cell membranes obtained from cells expressing both APP and BACE2 or can be isolated from cells expressing either APP or β-secretase and then combined together. Alternatively, APP and/or BACE2 may be partially or fully synthesized by traditional chemical synthesis and/or recombinant DNA technology.

[0094] In a special embodiment, cells engineered to recombinantly express APP or APP fragments of β-secretase processing or the C-terminal 100 residues of APP and/or BACE2 can be used. For example, following incubation of cells overexpressing BACE2/APP with the test compound, the supernatant is assayed for levels of soluble products of APP proteolysis, i.e., Aβ and/or β-NTF and/or p3, whereas cell membranes obtained by cell lysis are assayed for cell-associated products of APP proteolysis, i.e. CTFs (α-CTF or β-CTF). Detection of the APP proteolytic products can be accomplished using any of a number of methods to determine the absence or presence or altered amounts of the differentially expressed polypeptide in the test sample. In general, antibodies that specifically bind a differentially expressed polypeptide of the invention are added to a sample, and incubated for a period of time sufficient to allow binding to the epitope, usually at least about 30 minutes. The antibody can be detectably labeled for direct detection (e.g., using radioisotopes, enzymes, fluorescers, chemiluminescers, and the like), or can be used in conjunction with a second stage antibody or reagent to detect binding (e.g., biotin with horseradish peroxidase-conjugated avidin, a secondary antibody conjugated to a fluorescent compound, e.g., fluorescein, rhodamine, Texas Red, etc.). Any suitable alternative method of qualitative or quantitative detection of levels or amounts of differentially expressed polypeptide can be used, for example western blot, immunoprecipitation, radioimmunoassay, etc. In a preferred embodiment, an enzyme-linked immunosorbent assay (ELISA) is used to detect the presence of the APP proteolytic products, Aβ, p3, β-NTF and CTFs. Quantitation of multiple samples can be made more time efficient by running the assay in an ELISA format for rapid quantitation by spectrophotometric or colorimetric detection.

[0095] Cells overexpressing BACE2/APP or APP fragments of β-secretase processing or the C-terminal 100 residues of APP can be grown in 96-well tissue culture plates, exposed to various potential compounds at different concentrations and/or for different time, and an aliquot of culture supernatant taken for estimation of APP proteolytic products released from cells, i.e. Aβ, p3,and/or β-NTF, by ELISA. Cell-associated APP proteolytic products (CTFs, i.e. α-CTF or β-CTF) can be conveniently estimated by washing cells, lysing cells with mild detergent, washing away all the cytosolic contents, and estimating the amount of membrane-bound CTFs by carrying out ELISA in the same plate. If the compound reduces the level of Aβ and increases the level of CTFs (α-CTF and/or β-CTF) products, e.g., as compared with a previously known standard then the compound is a candidate for the treatment of patients with amyloid-associated disorders.

[0096] In a preferred embodiment, the present invention provides an assay methodology for identifying compounds which have an effect on (preferably enhance) BACE2-mediated suppression of Aβ by promoting α-secretase-like cleavage, using membrane-enzyme mixtures. In assays using cell-membranes, background levels of APP proteolytic products may be removed before the membranes are used in the assays. This step could be eliminated by precisely determining the level of APP proteolytic products in a known cell culture of cells expressing APP. Thereafter the known level can be adjusted for in the assay, i.e., increases or decreases relative to the known background level could be determined by subtracting away the known background level. In order to perform the assay in this manner, it would, of course, be necessary to obtain cell membranes from a statistically significant number of recombinant cells which express a known level of APP and thereafter determining the background level of APP proteolytic products present in the membranes of these cells.

[0097] The assays may be performed in the presence or absence of BACE1 and/or other β-secretase(s).

[0098] In a preferred embodiment, the present invention provides an assay methodology for identifying compounds which have an effect on (preferably enhance) BACE2-mediated suppression of Aβ by promoting α-secretase-like cleavage, using synthetic substrates spanning residues comprising the α-secretase site of APP. Such substrates might include, for example, synthetic peptides or fluorogenic synthetic substrates. Read-outs of such an assay might include the generation of a smaller peptide fragment or by fluorescence resonance energy transfer (FRET) of the cleaved fluorescently tagged substrate.

[0099] 3. Transgenic animal models

[0100] Compounds found to enhance or stimulate BACE2-mediated suppression of Aβ production can be further assayed in transgenic mammals. Transgenic animal models are well known in the art, and are described, for example, in Moran et al. Proc. Natl. Acad. Sci. USA 92: 5341-5345 (1995); Games et al. Nature 373: 523-527 (1995); Haiso et al. Science 274: 99-102 (1996), and in U.S. Pat. Nos. 5,387,742 and 5,912,410, the entire disclosures of which are hereby expressly incorporated by reference. Briefly, according to the method disclosed in the cited patents, cloned recombinant or synthetic DNA sequences related to the pathology of Alzheimer's disease are injected into fertilized mammalian eggs (preferably mouse eggs). The injected eggs are implanted in pseudo pregnant females and are grown to term to provide transgenic mice whose cells express proteins related to the pathology of Alzheimer's disease. The injected sequences are constructed having promoter sequences connected so as to express the desired protein in specific tissues of the transgenic mammal (most notably in nerve tissue). The proteins which are preferably ubiquitously expressed include: (1) Aβ-amyloid core precursor proteins; (2) Aβ-amyloid related precursor proteins; and (3) serine protease inhibitor. The transgenic mice provide useful models for studying compounds being tested for their usefulness in treating Alzheimer's disease and related conditions.

[0101] 4. Compounds of the invention

[0102] Compounds of the invention encompass numerous chemical classes, including but not limited to the compounds described herein with known function. Novel methods are provided which employ compounds that are effective in enhancing or activating BACE2-mediated suppression or inhibition of Aβ production.

[0103] Candidate compounds can be obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological compounds may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs.

[0104] Compounds for use in the method of invention may be small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate compounds comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate compounds often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate compounds are also found among biomoleculese including, but not limited to: peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.

[0105] Further details of the invention will be illustrated in the following non-limiting Examples.

EXAMPLES

[0106] The following examples are set forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.

Example 1 Materials and Methods used in the BACE2 Assays

[0107] 1. Cloning and coexpression of BACE and BACE2

[0108] BACE 2 was amplified from human brain cDNAs by Taq Polymerase Chain Reaction (PCR) using sequence information from PCT publication WO99/34004-A2. The amplified PCR product was cloned into pCRII -TOPO vector using TOPO TA cloning techniques (Invitrogen Co., San Diego, Calif.). Following restriction enzyme digestion, the BACE2 DNA fragment was sub-cloned into Not I and BamH I sites of mammalian expression vector pcDNA 3.1 (−). Restriction enzyme digestion pattern and sequence data confirmed the presence and orientation of the insert in pCDNA3.1(−)/BACE2. BACE was similarly cloned from human brain cDNAs using sequence information available from Vassar et al., [1999] ibid) to generate a mammalian expression vector pCDNA3.1 (−)/BACE.

[0109] Expression vectors containing BACE and BACE2 cDNAs were transfected into HEK293T cells in the presence of APP751sw or CT100 (Shoji et al., Science 258: 126-129 [1992]; Lichtenthaler et al., Proc. Natl. Acad. Sci. USA 96: 3053-3058 [1999]). Transfections were performed in 24 well plates using Lipofectamine Plus (Gibco/BRL, Bethesda, Md.) and DNA concentrations were kept constant by including non-specific DNA. Expression plasmids were tested for BACE and BACE2 expression by Western blotting. Cell culture supernatants were collected 48 hours and 72 hours post-transfection, and assayed for α-NTF, β-NTF and Aβ formation. β-NTF measurement was performed as described below. α-NTF was captured like β-NTF but was detected with biotinylated 2H3 (Johnson-Wood et al., Proc. Nati. Acad. Sci. USA 94: 1550-1555 [1997]). Aβ levels were determined by an ELISA using monoclonal antibodies 266 for capture and biotinylated 3D6 for detection (see Johnson-Wood et al., [1997] ibid for antibody epitope description). Aβ42, in contrast, was captured using 21F 12 and detected with biotinylated 3D6. Cell extracts prepared 72 hour post-transfection were separated by SDS-PAGE (Novex) and probed with CT695 (Zymed) for APP and CTFs as well as with an Aβ specific monoclonal antibody WO2 (kindly provided by K. Beyreuther; Ida et al., J. Biol. Chem. 271: 22908-22914 [1996]). Alternatively, co-transfection experiments using APP751sw and BACE or BACE2 were performed in the human neuroblastoma cell line, SK-N-MC, available from the American Type Culture Collection (ATCC).

[0110] 2. Membrane preparations

[0111] Membrane preparation is the first step in the isolation and purification or enrichment of β-secretases (BACE or BACE2) and the substrate (APP) since both of them are expressed as membrane integral proteins. Membrane preparations were generated from human embryonic kidney 293 cells (HEK293) expressing the 751 form of APP carrying the “Swedish” AD mutation (293/751sw). However, the protocol described below can be used for any cell type with only a minor modification. Cells were stored as cell pellets at −80° C. until used for the preparation.

[0112] Approximately 70-100 gram of cells (wet weight) were routinely used to generate 50-100 ml of enzyme substrate complex/mixture from membrane extracts. The cells were thawed and were resuspended through different iterations in a total volume of 12-15 ×vol/gram wet weight of TE/1X protease inhibitor cocktail (PIC) buffer [20 mM Tris-HCl/5 mM EDTA pH 8.5 (TE) with 1X PIC (1X PIC: 10 μM leupeptin, 1 μM aprotinin and 1 μM pepstatin, Boehringer Mannheim). Initially, the pellet was resuspended in ˜6-9 ×vol/gram wet weight and homogenized using a tissumizer (IKA Labortechnik, Staufen, Germany) at medium setting for three times one minute with intermittent cooling on ice. The homogenate was then distributed into different 50 ml Falcon tubes and was centrifuged for 10 minutes at 1500 rpm in a table centrifuge (Sorvall) at 4° C. After the centrifugation, the supernatant corresponding to a PNS (post-nuclear supernatant) was carefully removed and pooled into a fresh tube. In order to avoid disturbing the relatively loose pellet, approximately 10 ml of material were left in each tube including the pellet that contained unbroken cells and nuclei. The pellet and remaining supernatant was pooled and resuspended in the remainder of the homogenization buffer. The suspension was then subjected to another round of homogenization with the tissumizer followed by centrifugation and supernatant collection as described above. The resulting PNS was pooled with the previously saved material. If deemed necessary, an additional round of homogenization was included or the previously centrifuged material was spun again to recover all the supernatant efficiently. The membranes were then recovered as a pellet by centrifugation of the pooled PNS at 28,000 rpm (˜65,000 ×g) in a Ti45 rotor (Beckman, Palo Alto, Calif.) for 30-40 min at 4° C.

[0113] Membrane preparations as prepared above were treated with a mild detergent to reduce, preferably to undetectable levels, background APP proteolytic products. The membrane pellet was resuspended sequentially in a total of 12 ×vol/gram wet weight of TE/1X PIC in the presence of a final concentration of 0.02% saponin (added from a 0.5% saponin stock solution made in distilled water). The pellet was homogenized on ice by 13-18 strokes in a Kontes glass tissue homogenizer with a tight pestle (0.013-0.14 mm clearance). Treatment with the mild detergent saponin permeabilizes the membranes and thus releases lumenal soluble proteins. In particular, this preferably reduces, to undetectable levels, any background APP proteolytic products, such as β-NTF. Following homogenization of the membranes on ice, the suspension was centrifuged in a Ti45 rotor at 28,000 rpm (˜65,000 ×g) for 30-40 minutes. The saponin extract containing β-NTF was stored at −80° C. until it was further purified over a Q-HP column (similarly to the membrane extract described below) and the resulting fractions containing β-NTF were aliquoted and stored at −80° C. for use as a standard in ELISA. The pellet after the saponin extraction was resuspended again in TE/1X PIC, 0.02% saponin and treated as described, and this step was repeated until the membranes were washed in a total of 12 ×vol/gram cell paste.

[0114] Following the saponin extraction, the final membrane pellet (P2 pellet) was routinely frozen at −80° C. until further use. When needed, the frozen P2 pellet was thawed and resuspended in TE/1X PIC. Triton X100-R was added to a final concentration of 0.3% and the suspension was dounced on ice at least 12 times in a Kontes glass tissue homogenizer with a tight pestle (0.013-0.14 mm clearance). After the material had been suspended well, the solution was centrifuged at 32,000 rpm (˜100,000 ×g) for 45-60 minutes at 4° C. The solubilized membrane supernatant was collected, and the pellet discarded. The solubilized Triton X100 extract was then filtered through a 0.45 μm bottle-top filter to remove insoluble material (Schleicher & Schuill) and was partially purified on a 25 ml Q-HP Sepharose column (Pharmacia, Stamford, Conn.) in the following manner.

[0115] The detergent-treated membrane preparations from the above step were partially purified using a Q-HP Sepharose chromatography column (Pharmacia, Stamford, Conn.). The Q-HP column was equilibrated with 5-10 column volumes (CVs) of equilibration buffer [20 mM Tris/EDTA pH 8.5, 0.05% Triton X100-R] and the extract was loaded at 5 ml/minutes. The column was then washed with 5 CVs of equilibration buffer to remove non-specifically bound proteins. Proteins including APP and β-secretase were eluted from the column with a linear gradient from 0-1M NaCl in equilibration buffer [TE, 0.05% Triton X100-R] over 5 CVs and ˜8 ml fractions were collected. 1 ×PIC was added to the collection tubes prior to the run.

[0116] The total protein concentration for each sample was determined using a BCA protein test (Pierce, Rockford, Ill.), and a protein profile was also determined for the rinses and the elution. Alternatively, protein was followed with a UV monitor. Samples were run on an SDS-polyacrylamide gel for Western Blot analysis, and blotted with pAb369, an antibody which recognizes the C-terminus of APP (Gouras et al. Proc. Natl. Acad. Sci. USA 97: 1202-1205 [2000]). The saponin extract of washes was also blotted to analyze the βNTF using AF-20 series antibodies or equivalent. βNTF-specific antibodies were generated against the neoepitope produced by β-secretase cleavage of APP. The antibodies were generated against synthetic peptides, ISEVNL in the case of swedish isoform or ISEVKM in the case of wt substrate. The peptides were conjugated to a protein carrier via the N-terminal cysteine on the peptide, and used to immunize rabbits according to standard procedures. The resulting antisera were affinity purified using the peptide immunogens.

[0117] Individual fractions were then assayed for the presence of APP using an ELISA as well as for the presence of β-secretase using the native substrate assay as described below. Fractions containing APP and β-secretase were pooled as APP/β-secretase complex/mixture, aliquoted and stored at −80° C. for future use.

[0118] 3. Partial purification of APP substrates

[0119] A partial purification approach to obtain APP751sw or APP751wt substrate devoid of endogenous β-secretase activity is presented below. Expression vector containing APP751sw or APP751wt cDNA in pcDNA3.1 (commercially available from Invitrogen) was transiently transfected into HEK293 cells according to standard procedures. Transient transfection of APP751sw improved the separation since a significantly higher ratio of substrate to enzyme could be obtained. Cells were transfected in roller bottles by a transfection method recommended by the manufacturer using FuGene 6 (Boehringer Mannheim). The cells were harvested and the equivalent of ˜5-10 gms of cell paste was subjected to detergent extraction using the protocol described above. The detergent extract separated on a 1 ml Q- HP Sepharose column, as described above, contains both β-secretase and APP751 sw. The APP751 sw containing fractions were then pooled and the pool was diluted ˜8-10 fold with equilibration buffer [20 mM Tris/EDTA pH 8.5, 0.05% Triton X100-R] to reduce the salt from the previous chromatography step. The material was then loaded onto a Mono Q column that had been equilibrated. Non-specifically bound proteins were washed with 10 CVs of equilibration buffer and proteins were eluted with a 15 CV linear gradient from 0-1 M NaCl in equilibration buffer. Again, fractions were analyzed for the presence of APP751 sw as described in earlier. The β-secretase activity was assayed with exogenously added APP751sw substrate. This was necessary since otherwise β-secretase would not have been detectable in fractions that were very limited in APP751sw substrate. The mono Q step allowed the separation of the APP751sw substrate from the bulk of the endogenous β-secretase. Based on this procedure, we have routinely obtained APP751sw at concentrations of ˜4-6 μg/ml and use ˜3-8 μl per reaction to determine the β-secretase activity when substrate needs to be added back to the reaction mixture. The β-secretase activity devoid of substrate from this column was also pooled for additional experiments.

[0120] Th C-terminal 100 amino acids of APP can also be prepared as a substrate for BACE2 activity. This fragment has been successfully expressed in bacteria with an epitope tag at the C-terminus to facilitate purification (Higaki et al. J. Biol. Chem. 271: 31885-31893 [1996]).

[0121] 4. Generation of BACE2 Asp mutant

[0122] A single D110A BACE2 mutant was created in the parent vector pcDNA3.1 (−)/BACE2 using Stratagene's QuickChange site-directed mutagenesis kit. The following primers were used to introduce the change and the mutation was subsequently confirmed by DNA sequencing. 

What is claimed is:
 1. A method of modulating the enzymatic production of Aβ-amyloid peptide (Aβ) from Aβ-amyloid precursor protein (APP) or a fragment thereof, comprising contacting said APP or APP fragment with a BACE2 polypeptide or an agonist or antagonist thereof.
 2. The method of claim 1 wherein said APP is a native sequence human APP.
 3. The method of claim 2 wherein said APP is the 695-amino acid isotype.
 4. The method of claim 2 wherein said APP contains the Swedish mutation.
 5. The method of claim 1 wherein said APP fragment is β-CTF.
 6. The method of claim 1 wherein said BACE2 is a native sequence BACE2 polypeptide.
 7. A method of inhibiting the formation of a β-amyloid peptide (Aβ) from β-amyloid precursor protein (APP) or a fragment thereof, comprising contacting said APP of APP fragment with a BACE2 polypeptide or an agonist thereof.
 8. The method of claim 7 wherein said APP is a native sequence human APP.
 9. The method of claim 8 wherein said APP is the 695-amino acid isotype.
 10. The method of claim 8 wherein said APP contains the Swedish mutation.
 11. The method of claim 7 wherein said APP fragment is β-CTF.
 12. The method of claim 7 wherein said BACE2 is a native sequence BACE2 polypeptide.
 13. The method of claim 7 which is performed in the presence of an α-secretase activity.
 14. The method of claim 7 which is performed in the present of a γ-secretase activity.
 15. The method of claim 7 which is performed in the presence of a β-secretase activity other than BACE2.
 16. The method of claim 15 wherein said β-secretase activity in due to the presence of an enzyme having a pH optimum at about pH 6.5-7.0, and an estimated molecular weight of about 32-39 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts, or about 20-26 kDa as calculated from radiation inactivation analysis of human brain samples, with a candidate compound.
 17. The method of claim 15 wherein said β-secretase activity is due to the presence of a β-secretase enzyme having a pH optimum at about pH 4.5-5.0 and an estimated molecular weight of about 50-60 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts or human brain samples (BACE1).
 18. The method of claim 7 wherein said BACE2 is in isolated form.
 19. The method of claim 7 wherein said BACE2 is in immobilized or cell bound form.
 20. The method of claim 7 wherein the treatment is performed with an agonist of BACE2.
 21. The method of claim 20 wherein said agonist stimulates the production of BACE2.
 22. The method of claim 20 wherein said agonist enhances the activity of BACE2.
 23. The method of claim 20 wherein said agonist mimics the activity of BACE2.
 24. The method of claim 20 wherein said agonist is a small molecule.
 25. A method of inhibiting the release of a full-length β-amyloid (Aβ) polypeptide from β-amyloid precursor protein (APP) or a fragment thereof, comprising cleaving said APP or APP fragment by a BACE2 polypeptide or an agonist thereof at a site interfering with β-secretase processing of said APP or APP fragment.
 26. The method of claim 25 wherein said site is at or around the α-secretase cleavage site of native sequence APP or a fragment thereof.
 27. The method of claim 26 wherein said site is within about 10 amino acids on either side of said α-secretase cleavage site.
 28. A method for identifying a modulator of the enzymatic production of β-amyloid peptide (Aβ) from β-amyloid precursor protein (APP) or a fragment thereof, comprising contacting APP or an APP fragment and BACE2 with a candidate compound and monitoring the effect of the candidate compound on the production of Aβ.
 29. The method of claim 28 wherein said modulator is an inhibitor of Aβ production.
 30. The method of claim 29 wherein the effect of the candidate compound on the production of Aβ is monitored by measuring the amount of Aβ formed.
 31. The method of claim 29 which is performed in the presence of an α-secretase activity.
 32. The method of claim 29 which is performed in the presence of a γ-secretase activity.
 33. The method of claim 29 which is performed in the presence of a β-secretase activity other than BACE2.
 34. The method of claim 33 wherein said β-secretase activity is due to the presence of an enzyme having a pH optimum at about pH 6.5-7.0, and an estimated molecular weight of about 32-39 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts, or about 20-26 kDa as calculated from radiation inactivation analysis of human brain samples, with a candidate compound.
 35. The method of claim 33 wherein said β-secretase activity is due to the presence of a β-secretase enzyme having a pH optimum at about pH 4.5-5.0 and an estimated molecular weight of about 50-60 kDa as calculated from radiation inactivation analysis of HEK293 cell membrane extracts or human brain samples (BACE1).
 36. The method of claim 30 wherein the amount of Aβ formed is reduced by at least about 50%.
 37. The method of claim 30 wherein the amount of Aβ formed is reduced by at least about 75%.
 38. The method of claim 30 wherein the amount of Aβ formed is reduced by at least about 90%.
 39. The method of claim 29 further comprising the step of comparing the effect of the test compound on Aβ production with the effect of BACE2 in the absence of the test compound.
 40. The method of claim 39 wherein the test compound causes at least about 15% reduction in the amount of Aβ over the effect of BACE2 in the absence of the test compoud.
 41. The method of claim 40 wherein said reduction is at least about 25%.
 42. The method of claim 40 wherein said reduction is at least about 50%.
 43. The method of claim 40 wherein said reduction is at least about 75%.
 44. The method of claim 29 further comprising the step of comparing the effect of the test compound on Aβ production with Aβ production in the absence of BACE2.
 45. The method of claim 28 which is performed in a cell-free format.
 46. A modulator of the enzymatic production of Aβ-amyloid peptide (Aβ) from Aβ-amyloid precursor protein (APP) or a fragment thereof, identified by the method of claim
 29. 47. The modulator of claim 46 which is an inhibitor.
 48. The modulator of claim 46 which is a BACE2 agonist.
 49. The modulator of claim 46 which is a peptide or polypeptide.
 50. The modulator of claim 46 which is a small molecule.
 51. A method for reducing the amount of Aβ-amyloid deposits in the central nervous system (CNS) of a mammal comprising administering to said mammal an effective amount of BACE2 or an agonist thereof.
 52. The method of claim 51 wherein said mammal is human.
 53. The method of claim 52 wherein said deposits are in the brain.
 54. A method for the treatment of Alzheimer's disease (AD), an AD-type pathology or cerebral amyloid angiopathy in a mammalian patient, comprising administering to said patient an effective amount of BACE2 or an agonist thereof.
 55. The method of claim 54 wherein said patient is human.
 56. The method of claim 54 wherein said patient is at risk of developing Alzheimer's disease (AD), an AD-type pathology or cerebral amyloid angiopathy, and the treatment is prevention. 